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Niema Moshiri - Ph.D. Candidate
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Niema Moshiri

Ph.D. Candidate
University of California System • University of California, San Diego • San Diego • United States of America

Skills and expertise

Fields of interest
  • WGS analysis
  • De novo sequencing analysis
  • RNA-seq analysis
Languages
  • English
Programming languages
  • C
  • C++
  • Java
  • MATLAB
  • Python
  • R
  • Shell (Bash)

Favorites and Collections

Favorites

TreeCluster
Desktop
FAVITES
Desktop

Collections

No collections...

Bioinformatics projects

TOOLS MAINTAINED

TreeN93

Desktop

TreeN93

(0) 0 discussion(s)
Provides a threshold-free distance-based tool for inferring viral transmission clusters. TreeN93 proceeds by executing transmission cluster identification from pairwise TN93 distances. This software…
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TreeSwift

Desktop

TreeSwift

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Assists users in traversing and manipulating trees. TreeSwift is a package that consists of two classes: (i) a Node class, which contains the data and local relationships, and (ii) a Tree class,…

TreeCluster

Desktop

TreeCluster

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Deduces transmission clusters from a given phylogenetic tree inferred from viral sequences. TreeCluster reduces the number of clusters of leaves of a bifurcating phylogenetic tree through several…

Education

Ph.D. Bioinformatics and Systems Biology
University of California, San Diego
2015 - Today
B.S. Bioengineering: Bioinformatics (Minor in Economics)
University of California, San Diego
2011 - 2015

Fields of interest

WGS analysis
Allows users to perform reconstruction of phylogenetic trees and ancestral…
Analyses genome wide association studies (GWAS) signals and determines…
Allows users to map long readings with high error rates. lordFAST is designed…
De novo sequencing analysis
Serves as a fully automatic analysis of protein family conservation within a…
Identifies convergent changes. PCOC is based on the following definition: a…
Integrates multiple assayed transcription factors (TFs) bound/unbound DNA…
RNA-seq analysis
Integrates multi-omics profiles for phenotype prediction. iOmicsPASS utilizes…
Consists of a genomic context explorer. GeneSpy is a program that aims to…
Authorizes users to perform low-frequency variant calling. AIRVF is a…